5-150217392-C-T

Position:

• chr5-150217392-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000524041.1(SLC6A7):​c.1830-152C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,068 control chromosomes in the GnomAD database, including 4,679 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.25 (4679 hom., cov: 32)
• Consequence: SLC6A7 ENST00000524041.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258

Genes affected

SLC6A7 (HGNC:11054): (solute carrier family 6 member 7) This gene is a member of the gamma-aminobutyric acid (GABA) neurotransmitter gene family and encodes a high-affinity mammalian brain L-proline transporter protein. This transporter protein differs from other sodium-dependent plasma membrane carriers by its pharmacological specificity, kinetic properties, and ionic requirements. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.150217392C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC6A7	ENST00000524041.1	c.1830-152C>T		intron_variant		5		ENSP00000428200.1

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37286 AN: 151950 Hom.: 4680 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.240

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.245 AC: 37298 AN: 152068 Hom.: 4679 Cov.: 32 AF XY: 0.241 AC XY: 17916 AN XY: 74344

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.236

Alfa AF: 0.253 Hom.: 6835

Bravo AF: 0.248

Asia WGS AF: 0.138 AC: 479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.1
DANN	Benign	0.78

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs980272; hg19: chr5-149596955;